plotSpVar: Plot populations values against species values

In cati: Community Assembly by Traits: Individuals and Beyond

Plot populations values against species values

Description

Plot populations values against species values. The objectif is to see the contribution of intra-specific vs inter-specific variation to trait gradient.

Usage

	plotSpVar(traits = NULL, ind.plot = NULL, sp = NULL, variable = NULL, 
	col.ind = rgb(0.5, 0.5, 0.5, 0.5), col.pop = NULL, col.sp = NULL, 
	col.site = NULL, resume =  FALSE, p.val = 0.05, min.ind.signif = 10, 
	multipanel = TRUE, col.nonsignif.lm = rgb(0, 0, 0, 0.5), 
	col.signif.lm = rgb(1, 0.1, 0.1, 0.8), silent =  FALSE)

Arguments

traits	Individual Matrix of traits with traits in columns.
ind.plot	Factor defining the name of the plot in which the individual is.
sp	Factor defining the species which the individual belong to.
variable	A matrix of variables corresponding to each site (in rows) and each trait (in columns). If you want to plot all traits against one variable, variable can be a vector of numerical values.
col.ind	Color for individual values.
col.pop	Color for populational mean values.
col.sp	Color for species mean values.
col.site	Color for sites mean values.
resume	Logical, if TRUE plot a simple form of the plot.
p.val	Choosen p.value to print significant linear relationship using linear model. Argument past to the lm funtion internally.
min.ind.signif	Minimum individual to print significant linear relationship.
multipanel	Logical value. If TRUE divides the device to shown several traits graphics in the same device.
col.nonsignif.lm	Color for non significant linear relationship.
col.signif.lm	Color for significant linear relationship.
silent	Logical value, if resume = FALSE do not print warning argument.

Value

None; used for the side-effect of producing a plot.

Author(s)

Adrien Taudiere

See Also

plotDistri

Examples

	data(finch.ind)
	
	#Random variable for this example
	variable <- c(1,5,15,6,3,25)
	## Not run: 
	plotSpVar(traits.finch, ind.plot.finch, sp.finch, variable, 
	silent = TRUE)

	#If we change the value of the threshold 
	#(alpha = 10% instead of 5% 
	#and the minimum individual to represent significativity 
	#fixed to 3 instead of 10 by default) 
	#we can see some significant relationships.

	plotSpVar(traits.finch, ind.plot.finch, sp.finch, variable, 
	p.val = 0.1,  min.ind.signif = 3, silent = TRUE)


	#For a more simple figure, add the option resume = TRUE. 
	#Again if we change the value of the threshold 
	#(alpha = 10% instead of 5% 
	#and the minimum individual to represent significativity
	# fixed to 3 instead of 10 by default) 
	#we can see some significant relationships.

	plotSpVar(traits.finch, ind.plot.finch, sp.finch, variable, 
	silent = TRUE, resume = TRUE, col.pop = "grey")
	
	plotSpVar(traits.finch, ind.plot.finch, sp.finch, variable, 
	silent = TRUE, resume = TRUE, col.pop = "grey", col.sp = "black")
	
	plotSpVar(traits.finch, ind.plot.finch, sp.finch, variable, 
	silent = TRUE, resume = TRUE, col.pop = "grey", col.sp = "black", 
	p.val = 0.1,  min.ind.signif = 3)

## End(Not run)

cati documentation built on March 18, 2022, 5:43 p.m.